Table of Contents

Apple Command Line Tools

Apple provides a suite of “command line tools” to facilitate computer programming, and these tools include git which we will use for this workshop. To install the command line tools, open the Terminal application by searching for “Terminal” in Spotlight:

Search for Terminal in Mac Spotlight

A note on using Terminal: Terminal will likely (and often atwhen you first start using it!) prompt you messages like, “Terminal would like to access files on Desktop.” If/when you see this message, always agree! Agreeing allows your Terminal to access your computer’s file system.

When Terminal is open, type xcode-select --install into the Terminal and press Enter, which will reveal a message as follows:

xcode-select --install

Shortly after, a separate window will pop up prompting you to install command line tools, where you should click Install:

xcode-select --install popup

A license agreement will then appear, which you should Agree to in order to continue with the installation:

xcode-select --install license

Finally, command line tools will install, and you can follow its progress in this window that will appear. Importantly, this screen tends to first appear with outrageous installation times, like 165 hours (!) below. Don’t panic! These outrageous times will drop quickly, and the whole process will really take about 10-20 minutes.

xcode-select --install installing

R and RStudio

This workshop does not require a specific R or RStudio version for this workshop. If you already have R and RStudio installed, you can skip this section!

Installing R

First, navigate to the CRAN website in the browser: https://cran.r-project.org/. Click the link Download R for macOS:

CRAN Landing Page

On the next page, click the link to install the Intel 64-bit of R, R-4.2.0.pkg (blue box in the image below). This Intel version will still work on M1 computers. We do NOT recommend installing the Apple silicon arm64 (crossed out in the image below) build because it tends to conflict with some Bioconductor packages which you may want to use in your own research.

Website with link to download R

Open the downloaded R installer, and follow instructions to install R onto your computer. Make sure to agree to the license in the setup menu and give your computer’s password when prompted! R 4.2.0 Installer

Installing the RStudio IDE

First, navigate to the RStudio Download page website in the browser: https://www.rstudio.com/products/rstudio/download/. Click the link to Download the Free version of RStudio Desktop.

RStudio Download Page

Next, click the large link to Download RStudio for Mac:

RStudio Download Page

Open the downloaded RStudio installer, and follow instructions to install it onto your computer. Note that if you’re using an Apple Silicon (M1) chip, you may be prompted to install something called Rosetta 2 in order to use RStudio. Rosetta 2 is a software made by Apple to support the Intel to M1 transition, and it is currently needed to run RStudio on M1 chips. If prompted to install Rosetta 2, agree to the prompt and follow instructions accordingly.

Installing necessary R packages

For this workshop, you will need to have the following R packages installed: + tidyverse + rmarkdown + optparse + renv

If you already have these packages installed, you’re good to go!

Otherwise, open RStudio (this assumes both R and RStudio have been installed). You can check if these packages are installed by scrolling through the Packages tab in the bottom-right pane of RStudio. If you see the package of interest listed, then you know it’s installed. For example, the image below tells us that optparse is already installed and no additional action is required to install this package:

Shows that the optparse package is already installed on this computer

If you need to install any of the require packages, use the function install.packages() in Console, as follows:

# Install optparse only:
install.packages("optparse")

# Install rmarkdown only:
install.packages("rmarkdown")

# Install tidyverse only:
install.packages("tidyverse")

# Install renv only:
install.packages("renv")

# Or, you can install several simultaneously
# For example, this installs optparse and renv :
install.packages(c("optparse", "renv"))

After running this/these command(s), you will see some progress messages pass in Console (maybe in a different color from this image, but that’s ok!!). The following image shows, for example, what these messages look like for a successful installation of optparse:

Shows the process and output for installing the optparse package

Note: While installing packages, you may be prompted to install Command Line Tools if you didn’t install it already. If you see this message, agree to it and follow all installation steps for Command Line Tools.

GitKraken

We will use the GUI (graphical user interface) called GitKraken to work with git in this workshop. This GUI can be installed from https://www.gitkraken.com/, where you can click “Download GitKraken Client Free” (do not pay!!):

GitKraken Landing Page

Then, select the appropriate version for your computer’s architecture.

GitKraken Download options

The GitKraken installer will now download, and when completed, open it and follow all installation instructions.

A suitable text editor

macOS comes with a “text editor” program called “TextEdit.” In spite of its compelling name, this is NOT a recommend text editor for writing computer code! Please do not use TextEdit!

Instead, we recommend you obtain one of the following (free versions!) of these more robust text editors: